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techniques for eliciting differentially expressed
genes. We conclude with classification techniques
that were employed on combined datasets.
data on primary human keratinocytes receptors for
the cytokines IL-19, IL-20, IL-22, and IL-24 (Sa
et al., 2007). The effects of all cytokines on cul-
tured human keratinocytes and in a reconstituted
human epidermal culture system were evaluated
by comparison with controls.
In the GSE6475 serie, the gene expression
profiles in acne patients were studied in order to
identify the specific genes involved in inflamma-
tory acne (Trivedi et al., 2006). Skin biopsies were
obtained from an inflammatory papule and from
normal skin in six patients with acne. Biopsies were
also taken from normal skin of six subjects without
acne. Gene array expression profiling was led to
compare lesional with nonlesional skin in acne
patients, and nonlesional skin from acne patients
with skin from normal subjects. This experiment
studied gene expression changes in inflammatory
acne lesions and potential therapeutic targets in
inflammatory acne.
To characterize the molecular effects of IL-1
in epidermis, the GSE9120 serie studied the hu-
man epidermal keratinocytes treated with IL-1a
compared to control cells at 1h, 4h, 24h, and 48h
time points (Yano et al., 2008). This comparative
analysis was led for comprehensive investiga-
tions defining the targets of IL-1 in epidermal
keratinocytes and understanding the nature of the
inflammatory response and the gene products that
mediate the effects of IL-1 in these cells.
Description of Data Sets
We consider four experiments series (GSE6281,
GSE7216, GSE6475 and GSE9120) available
on the GEO website. These data are related to
skin reactions; they come from 85 Affymetrix
micro-arrays (either HG-U133 Plus 2.0 array or
HG-U133A 2.0 array) experiments on human skin
allergic contact dermatitis. In both series GSE6281
and GSE7216, cRNAs were extracted from skin
biopsies and a genome wide expression analysis
was carried out on the same HG-U133 Plus 2.0
array (platform GPL570) gene chip containing
54675 probe sets, while the hybridized cRNA of
series GSE6475 and GSE9120 were prepared us-
ing the gene chip HG-U133A 2.0Array containing
22277 probe sets. Table 2 provides some details
on these datasets.
The GSE6281 serie introduced in (Pedersen
et al., 2007) used a high density oligonucleotide
array for gene expression profiling in human skin
during the elicitation of allergic contact dermatitis.
Samples are part of an analysis of gene expression
time-course. Skin biopsies from normal and nickel-
exposed skin were obtained from 7 nickel-allergic
patients and 5 non-allergic controls at four different
time points 0h, 7h, 48h and 96h during elicitation
of eczema. In addition, one nickel-allergic patient
and one healthy control were recruited for im-
munocytochemistry study.
The GSE7216 serie contains gene expression
Procedure of Integration
The variability in experimental environments such
as RNA sources, micro-array production, or the
Table 2. Characteristics of example datasets
Series
Affymetrix
Data Type
Nb of probesets
Description
Size
GSE6281
U133 Plus 2.0
Raw Data
54675
Contact Allergy
34
GSE7216
U133 Plus 2.0
Raw Data
54675
IL-10 Cytokine Family
25
GSE6475
U133A 2.0
Raw Data
22277
ACNE
18
GSE9120
U133A 2.0
Raw Data
22277
Keratinocytes+I1b
8
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